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- PDB-5y3m: Crystal structure of bovine TLR9 in complex with two DNAs (CpG DN... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5y3m | ||||||
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Title | Crystal structure of bovine TLR9 in complex with two DNAs (CpG DNA and TCGTTT DNA) | ||||||
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![]() | IMMUNE SYSTEM / Innate immunity / Toll-like receptor / Leucine-rich repeat / DNA binding | ||||||
Function / homology | ![]() regulation of B cell differentiation / endolysosome / positive regulation of toll-like receptor 9 signaling pathway / positive regulation of B cell activation / unmethylated CpG binding / siRNA binding / early phagosome / pattern recognition receptor activity / positive regulation of immunoglobulin production / toll-like receptor signaling pathway ...regulation of B cell differentiation / endolysosome / positive regulation of toll-like receptor 9 signaling pathway / positive regulation of B cell activation / unmethylated CpG binding / siRNA binding / early phagosome / pattern recognition receptor activity / positive regulation of immunoglobulin production / toll-like receptor signaling pathway / canonical NF-kappaB signal transduction / positive regulation of interferon-alpha production / positive regulation of B cell proliferation / activation of innate immune response / positive regulation of interferon-beta production / positive regulation of interleukin-6 production / positive regulation of type II interferon production / positive regulation of NF-kappaB transcription factor activity / defense response to virus / positive regulation of MAPK cascade / lysosome / endosome / inflammatory response / innate immune response / endoplasmic reticulum membrane / endoplasmic reticulum / protein homodimerization activity / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ohto, U. / Shimizu, T. | ||||||
![]() | ![]() Title: Toll-like Receptor 9 Contains Two DNA Binding Sites that Function Cooperatively to Promote Receptor Dimerization and Activation Authors: Ohto, U. / Ishida, H. / Shibata, T. / Sato, R. / Miyake, K. / Shimizu, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 583.8 KB | Display | ![]() |
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PDB format | ![]() | 479 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 492.2 KB | Display | ![]() |
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Full document | ![]() | 498.5 KB | Display | |
Data in XML | ![]() | 49.5 KB | Display | |
Data in CIF | ![]() | 69.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5y3jC ![]() 5y3kC ![]() 5y3lC ![]() 3wpeS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: THR / End label comp-ID: THR / Refine code: _ / Auth seq-ID: 28 - 801 / Label seq-ID: 8 - 781
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Components
#1: Protein | Mass: 89323.531 Da / Num. of mol.: 2 / Fragment: UNP residues 25-817 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: DNA chain | Mass: 1790.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: DNA chain | Mass: 3066.012 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #4: Sugar | ChemComp-NAG / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 54.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 10%(w/v) PEG 4000 0.5M NaCl 0.1M Mes-NaOH pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 22, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→48.96 Å / Num. obs: 62911 / % possible obs: 99.9 % / Redundancy: 5.1 % / Net I/σ(I): 8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3WPE Resolution: 2.5→48.96 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.9 / SU B: 24.732 / SU ML: 0.244 / Cross valid method: THROUGHOUT / ESU R: 0.611 / ESU R Free: 0.281 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.77 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→48.96 Å
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Refine LS restraints |
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